I'm a bioinformatics post-doc in Prof Sandrine Da Cruz's lab at the VIB-KU Leuven Center for Neuroscience (Belgium), mainly focusing on transcriptomic analysis (gene expression, alternative splicing and polydenylation) of in vitro and in vivo models of amyotrophic lateral sclerosis (ALS) to uncover novel disease effectors. I previously completed a PhD in the labs of Prof Pietro Fratta & Dr Maria Secrier at University College London studying alternative polyadenylation (APA) in ALS, mainly using bulk RNA-seq data.
Interested in and working on:
- Developing improved methods for identifying, quantifying and assessing differential usage of polyadenylation sites from bulk RNA-seq data
- Developing generic omic analysis toolkits built on top of existing bioinformatics libraries, in particular the wonderful pyranges(1) library
- developing and benchmarking tools for investigating alternative polyadenylation using any flavour of RNA-sequencing (lots of ideas, too little time... get in touch if you're interested in collaborating!)
- Snakemake (building and deploying pipelines and developing tools to make it easier to do so)
- RNA processing in general
- Working out how best to use AI in my daily work (focusing on software development at the moment...)
Previous major projects:
- Analysis of APA dysregulation in ALS - Developed analysis pipelines in Snakemake (e.g. PAPA, QAPA_snakemake, bulk_polya_tail_reads, bedops_parse_star_junctions, rna_seq_single_steps) and analysis code (tdp43-apa, thesis)
- APAeval - a community project to develop a framework for reproducible benchmarking of bioinformatic algorithms and assess the performance of tools that identify and/or quantify polyA sites from bulk RNA-seq data.